The domain of organic chemistry is to study carbon-containing compounds

Biochemistry studies the chemistry of living systems

Carbon atom is the most important atoms in biological molecules

Valence of four, lacking four electron at its outermost electron orbital

Methods of satisfaction of stable status: electron sharing with other electron deficient atoms (such as other carbon atoms) -- formation of covalent bonds with “light” elements (such as carbon, oxygen, hydrogen, and nitrogen) to form stable compounds as relative to their atom weight.

Single bonds, double bonds and triple bonds

Fig. 2-1 Electron configuration of some biologically important atoms and molecules

3.
Carbon-Containing Molecules Are Stable Energies of biologically important transitions, bonds, and wavelengths of electromagnetic radiations

Calorie: amount of energy needed to raise the temperature of one gram of water one degree centigrade

4.
The Carbon-carbon bonds are the fittest for the biological chemistry under solar radiation

The relationship of electromagnetic radiation and the wavelength: E = 28,600/  (E, kcal/einstein;  , nm; 28,600, the constant with the units of kcal-nm/einstein, an einstein is equal to 1 mole of photons)

A tetrahedral structure of carbon atoms have geometric symmetry - when four different atoms or groups of atoms are bonded to the four corners of such a tetrahedral structure, two different spatial configurations are possible, but not superimposable

An asymmetric carbon atom has four different substituents. Both L- and D-alanine present in nature but only L- type is present in proteins. D-glucose has four asymmetric carbon atom and has 2 4 or 16 kinds of possible stereoisomers.

Water is the single most abundant component of cells and organisms. 75-85% of a cell is water (10-20 in spores and dry seeds)

The polarity of water molecules are caused by the angles that hydrogen atom bond to the oxygen atom (104.5 0 ), making the oxygen atom electronegative (  - ). This property accounts for the cohesiveness, the temperature-stabilizing capacity and the solvent properties of water .

Water molecules are cohesive -- Hydrogen bonds form between the hydrogen atoms and the oxygen atoms of water molecules and are responsible for its high boiling point, high specific heat, and high heat of vaporization .

Water has a high temperature-stabilizing capacity -- Specific heat is the amount of heat a substance absorb per gram to increase its temperature 1 0 C. The specific heat of water is 1.0 calorie per gram.

Water has a high heat of vaporization, the amount of energy required to convert one gram of a liquid into vapor.

Water is an excellent solvent. A solvent is a fluid in which another substance, called the solute , can be dissolved.

Hydrophobic: “water fearing”

Hydrophilic: “water loving”

The solubilization of sodium chloride because water molecules form spheres of hydration More properties of water originated from its polarity

Macromolecules: proteins, ribonucleic acids (DNA or RNA), and polysaccharides (starch, glycogen, and cellulose), and lipid (?, with different synthesizing method)

Macromolecules are responsible for most of the form and function in living systems. They are, however, generated by polymerization of small organic molecules, a fundamental principle of cellular chemistry

The monomers: glucose, amino acids, nucleotides

Informational macromolecules: DNA and proteins

Storage macromolecules & structural macromolecules

12.
Macromolecules are synthesized by stepwise polymerization of monomers The basic principles for the synthesis of macromolecules: 1. Macromolecules are synthesized by stepwise polymerization of similar or identical monomers 2. The addition of each monomeric units occurs with the removal of a H2O molecule -- condensation reaction 3. Momomeric units are activated 4. Activation usually involves coupling of monomers to carrier molecule 5. ATP (adenosine phosphate provides energy ) 6. Directionality of macromolecules

13.
The importance of self-assembly The principle of self-assembly: the information required to specify the folding of macromolecules and their interactions to form more complicated structures with specific biological functions is inherent in the polymers themselves